• Bioconductor – A plethora of tools for analysis and comprehension of high-throughput genomic data, including 1500+ software packages. [ paper-2004 | web ]
• Biopython – Freely available tools for biological computing in Python, with included cookbook, packaging and thorough documentation. Part of the Open Bioinformatics Foundation. Contains the very useful Entrez package for API access to the NCBI databases. [ paper-2009 | web ]
• Bioconda – A channel for the conda package manager specializing in bioinformatics software. Includes a repository with 3000+ ready-to-install (with conda install) bioinformatics packages. [ paper-2018 | web ]
• BioJulia – Bioinformatics and computational biology infastructure for the Julia programming language. [ web ]
• Rust-Bio – Rust implementations of algorithms and data structures useful for bioinformatics. [ paper-2016 ]
• SeqAn – The modern C++ library for sequence analysis.

The Taverna suite is written in Java and includes the Taverna Engine(used for enacting workflows) that powers both the Taverna Workbench(the desktop client application) and the Taverna Server (which allows remote execution of workflows). Taverna is also available as a Command Line Tool for a quick execution of workflows from a terminal.

Address of the bookmark: http://www.taverna.org.uk/

Gargi believes in its mission statement that every student who passes through the portals of the college emerges as a wholly developed individual symbolizing the spirit of enterprise and inquiry that characterizes Gargi.

Bioinformatics Infrastructure Facility (BIF), Gargi College, University of Delhi invites candidates for filling up the following purely temporary positions sponsored by DBT, New Delhi.

1. Name of the post: Traineeship
Essential Qualification: Post Graduate degree in Bioinformatics or any other branch of Life Sciences preferably with dissertation in Bioinformatics.
Desirable Qualification: Prior knowledge of programming languages such as C, VB, SQL etc. and software/database development.

2. Name of the post: Research Associate
Essential Qualification: PhD in Bioinformatics/Biological Sciences/Computer Science or allied sciences with proven experience in bioinformatics.

3. Name of the post: Studentship
Essential Qualifications: Final year Post Graduate students pursuing a degree in Bioinformatics or any branch of Life Science with knowledge of bioinformatics.

How to apply:
Interested candidates are required to appear for the walk in interview on 29th Aug, 2013 at 10.00 AM in Principal’s Office, Gargi College, Sirifort Road, N. Delhi-110049, with their CVs, original documents and a set of Photostat copies of all original documents.

http://www.du.ac.in/fileadmin/DU/students/Pdf/du/advt/2013/16082013_Gargi_RAplus2_Advt.pdf

• the Damerau–Levenshtein distance allows insertion, deletion, substitution, and the transposition of two adjacent characters;
• the longest common subsequence (LCS) distance allows only insertion and deletion, not substitution;
• the Hamming distance allows only substitution, hence, it only applies to strings of the same length.
• the Jaro distance allows only transposition.

use Text::Levenshtein qw(distance);

 print distance("foo","four");
 # prints "2"

 my @words     = qw/ four foo bar /;
 my @distances = distance("foo",@words);

 print "@distances";
 # prints "2 0 3"

use Algorithm::LCSS qw( LCSS CSS CSS_Sorted );
    my $lcss_ary_ref = LCSS( \@SEQ1, \@SEQ2 );  # ref to array
    my $lcss_string  = LCSS( $STR1, $STR2 );    # string
    my $css_ary_ref = CSS( \@SEQ1, \@SEQ2 );    # ref to array of arrays
    my $css_str_ref = CSS( $STR1, $STR2 );      # ref to array of strings
    my $css_ary_ref = CSS_Sorted( \@SEQ1, \@SEQ2 );  # ref to array of arrays
    my $css_str_ref = CSS_Sorted( $STR1, $STR2 );    # ref to array of strings

There are many different modules on CPAN for calculating the edit distance between two strings. Here's just a selection.

Text::LevenshteinXS and Text::Levenshtein::XS are both versions of the Levenshtein algorithm that require a C compiler, but will be a lot faster than this module.

The Damerau-Levenshtein edit distance is like the Levenshtein distance, but in addition to insertion, deletion and substitution, it also considers the transposition of two adjacent characters to be a single edit. The module Text::Levenshtein::Damerau defaults to using a pure perl implementation, but if you've installed Text::Levenshtein::Damerau::XS then it will be a lot quicker.

Text::WagnerFischer is an implementation of the Wagner-Fischer edit distance, which is similar to the Levenshtein, but applies different weights to each edit type.

Text::Brew is an implementation of the Brew edit distance, which is another algorithm based on edit weights.

Text::Fuzzy provides a number of operations for partial or fuzzy matching of text based on edit distance. Text::Fuzzy::PP is a pure perl implementation of the same interface.

String::Similarity takes two strings and returns a value between 0 (meaning entirely different) and 1 (meaning identical). Apparently based on edit distance.

Text::Dice calculates Dice's coefficient for two strings. This formula was originally developed to measure the similarity of two different populations in ecological research.

awk '/pattern1/ {Actions}
/pattern2/ {Actions}' file

The working of Awk is as follows
Awk reads the input files one line at a time.
For each line, it matches with given pattern in the given order, if matches performs the corresponding action.
If no pattern matches, no action will be performed.
In the above syntax, either search pattern or action are optional, But not both.
If the search pattern is not given, then Awk performs the given actions for each line of the input.
If the action is not given, print all that lines that matches with the given patterns which is the default action.
Empty braces with out any action does nothing. It wont perform default printing operation.
Each statement in Actions should be delimited by semicolon.
Say you have data.tsv with the following contents:

$ cat data/test.tsv
contig1 ACTGTCTGTCACTGTGTTGTGATGTTGTGTGTG
contig2 ACTTTATATATT
contig3 ACTTATATATATATA
contig4 ACTTATATATATATA
contig5 ACTTTATATATT
By default Awk prints every line from the file.

$ awk '{print;}' data/test.tsv
contig1 ACTGTCTGTCACTGTGTTGTGATGTTGTGTGTG
contig2 ACTTTATATATT
contig3 ACTTATATATATATA
contig4 ACTTATATATATATA
contig5 ACTTTATATATT
We print the line which matches the pattern contig3

$ awk '/contig3/' data/test.tsv
contig3 ACTTATATATATATA
Awk has number of builtin variables. For each record i.e line, it splits the record delimited by whitespace character by default and stores it in the $n variables. If the line has 5 words, it will be stored in $1, $2, $3, $4 and $5. $0 represents the whole line. NF is a builtin variable which represents the total number of fields in a record.

$ awk '{print $1","$2;}' data/test.tsv
contig1,ACTGTCTGTCACTGTGTTGTGATGTTGTGTGTG
contig2,ACTTTATATATT
contig3,ACTTATATATATATA
contig4,ACTTATATATATATA
contig5,ACTTTATATATT

$ awk '{print $1","$NF;}' data/test.tsv
contig1,ACTGTCTGTCACTGTGTTGTGATGTTGTGTGTG
contig2,ACTTTATATATT
contig3,ACTTATATATATATA
contig4,ACTTATATATATATA
contig5,ACTTTATATATT

Awk has two important patterns which are specified by the keyword called BEGIN and END. The syntax is as follows:

BEGIN { Actions before reading the file}
{Actions for everyline in the file}
END { Actions after reading the file }

For example,
$ awk 'BEGIN{print "Header,Sequence"}{print $1","$2;}END{print "-------"}' data/test.tsv
Header,Sequence
contig1,ACTGTCTGTCACTGTGTTGTGATGTTGTGTGTG
contig2,ACTTTATATATT
contig3,ACTTATATATATATA
contig4,ACTTATATATATATA
contig5,ACTTTATATATT
-------
We can also use the concept of a conditional operator in print statement of the form print CONDITION ? PRINT_IF_TRUE_TEXT : PRINT_IF_FALSE_TEXT. For example, in the code below, we identify sequences with lengths > 14:

$ awk '{print (length($2)>14) ? $0">14" : $0"<=14";}' data/test.tsv
contig1 ACTGTCTGTCACTGTGTTGTGATGTTGTGTGTG>14
contig2 ACTTTATATATT<=14
contig3 ACTTATATATATATA>14
contig4 ACTTATATATATATA>14
contig5 ACTTTATATATT<=14
We can also use 1 after the last block {} to print everything (1 is a shorthand notation for {print $0} which becomes {print} as without any argument print will print $0 by default), and within this block, we can change $0, for example to assign the first field to $0 for third line (NR==3), we can use:

$ awk 'NR==3{$0=$1}1' data/test.tsv
contig1 ACTGTCTGTCACTGTGTTGTGATGTTGTGTGTG
contig2 ACTTTATATATT
contig3
contig4 ACTTATATATATATA
contig5 ACTTTATATATT
You can have as many blocks as you want and they will be executed on each line in the order they appear, for example, if we want to print $1 three times (here we are using printf instead of print as the former doesn't put end-of-line character),

$ awk '{printf $1"\t"}{printf $1"\t"}{print $1}' data/test.tsv
contig1 contig1 contig1
contig2 contig2 contig2
contig3 contig3 contig3
contig4 contig4 contig4
contig5 contig5 contig5
Although, we can also skip executing later blocks for a given line by using next keyword:

$ awk '{printf $1"\t"}NR==3{print "";next}{print $1}' data/test.tsv
contig1 contig1
contig2 contig2
contig3
contig4 contig4
contig5 contig5

$ awk 'NR==3{print "";next}{printf $1"\t"}{print $1}' data/test.tsv
contig1 contig1
contig2 contig2

contig4 contig4
contig5 contig5
You can also use getline to load the contents of another file in addition to the one you are reading, for example, in the statement given below, the while loop will load each line from test.tsv into k until no more lines are to be read:

$ awk 'BEGIN{while((getline k <"data/test.tsv")>0) print "BEGIN:"k}{print}' data/test.tsv
BEGIN:contig1 ACTGTCTGTCACTGTGTTGTGATGTTGTGTGTG
BEGIN:contig2 ACTTTATATATT
BEGIN:contig3 ACTTATATATATATA
BEGIN:contig4 ACTTATATATATATA
BEGIN:contig5 ACTTTATATATT
contig1 ACTGTCTGTCACTGTGTTGTGATGTTGTGTGTG
contig2 ACTTTATATATT
contig3 ACTTATATATATATA
contig4 ACTTATATATATATA
contig5 ACTTTATATATT
You can also store data in the memory with the syntax VARIABLE_NAME[KEY]=VALUE which you can later use through for (INDEX in VARIABLE_NAME) command:

$ awk '{i[$1]=1}END{for (j in i) print j"<="i[j]}' data/test.tsv
contig1<=1
contig2<=1
contig3<=1
contig4<=1
contig5<=1

POSITIONS OPEN FOR TEMPORARY RESEARCH PROJECT POSTS

(Date of interview 23rd September 2013 at 10:30 AM)

CSIR-Institute of Genomics & Integrative Biology (IGIB), desires to engage qualified incumbents on purely temporary basis as detailed below:

Project Code/Title (Project Code BSC0123)

Genome dynamics in Cellular Organization, Differentiation and Enantiostasis (GENCODE)

Project Fellow

First Class M.Sc./M.Tech in bioinformatics/Human Genetics/Genomics

Rs. 16,000/- + 30 % HRA per month

Sr. Project Fellow

First Class M.Sc./M.Tech in bioinformatics/Human Genetics/Genomics

With two years of experience in NGS data analysis.

Rs. 18,000/- + 30 % HRA per month

Age relaxation as per Govt. of India instructions.

Engagement is for the project and on behalf of the funding agency and the tenure shall be as mentioned above. The duration of the post is initially for One year or till the closing date of the project, whichever is earlier. Tenure may be extendable up to project duration. Contract may be terminated at any time by giving one-month notice by either side. The applicants will have no claim implicit or explicit for consideration against any CSIR/IGIB post.

How to Apply:

It is mandatory for eligible applicants to apply by both the processes as given below:

1. Sending the resume in MS Word format directly to hrd@igib.res.in (Mentioning the Project Code-Post Code in the Subject Line of the email example:GAP0059-1)

2. They also need to fill up proforma by clicking on the following link HR Online Form.

3. Candidate cannot apply for more than two posts.

Last date of receiving application is 02-09-2013.

No application would be entertained with result awaited status or after due date.

The email will be sent to the short listed candidates.

No TA/DA will be paid to the candidates to attend the interview. The engagement shall be as per guidelines of CSIR/Funding agency. Candidates will have an option to give reply in Hindi.

Note: The shortlisted candidates, who will receive the email for interview, have to report at 09:00 AM on the day of interview along with any Photo ID card and original certificates for entry purpose. Entry will be closed by 10:00 AM.

More @ http://www.igib.res.in/sites/default/files/23092013.htm

https://edu.t-bio.info/collaborative-model-bioinformatics-education-combining-biologically-inspired-bioinformatics-project-based-learning/

Address of the bookmark: http://www.biotnet.org/training-materials/python-programmers